AutoCloner

Multiple sequence alignment - TraesCS4A01G490100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS4A01G490100	chr4A	100.000	2369	0	0	1	2369	740458249	740455881	0.000000e+00	4375.0
1	TraesCS4A01G490100	chr4A	95.151	928	42	1	1445	2369	741795905	741794978	0.000000e+00	1461.0
2	TraesCS4A01G490100	chr4A	95.043	928	43	1	1445	2369	741589050	741589977	0.000000e+00	1456.0
3	TraesCS4A01G490100	chr4A	94.967	914	43	1	1445	2355	740022105	740021192	0.000000e+00	1430.0
4	TraesCS4A01G490100	chr4A	93.959	927	53	1	1446	2369	739650677	739651603	0.000000e+00	1399.0
5	TraesCS4A01G490100	chr4A	93.851	927	54	1	1446	2369	741485579	741484653	0.000000e+00	1393.0
6	TraesCS4A01G490100	chr4A	93.420	927	58	1	1446	2369	742055956	742056882	0.000000e+00	1371.0
7	TraesCS4A01G490100	chr4A	91.581	487	35	1	876	1356	740022713	740022227	0.000000e+00	667.0
8	TraesCS4A01G490100	chr4A	89.571	489	45	1	878	1360	740268916	740269404	1.200000e-172	616.0
9	TraesCS4A01G490100	chr4A	89.474	494	43	3	876	1360	740926846	740927339	1.200000e-172	616.0
10	TraesCS4A01G490100	chr4A	89.366	489	46	1	878	1360	740346321	740346809	5.600000e-171	610.0
11	TraesCS4A01G490100	chr4A	89.366	489	43	3	878	1360	740303069	740303554	7.240000e-170	606.0
12	TraesCS4A01G490100	chr4A	89.139	488	48	3	876	1359	739860786	739861272	9.370000e-169	603.0
13	TraesCS4A01G490100	chr4A	76.800	625	81	40	527	1109	739920984	739920382	2.300000e-75	292.0
14	TraesCS4A01G490100	chr4A	84.663	163	18	5	360	518	739921829	739921670	3.150000e-34	156.0
15	TraesCS4A01G490100	chr4A	85.124	121	9	7	1305	1425	739861434	739861545	5.350000e-22	115.0
16	TraesCS4A01G490100	chr4A	85.124	121	9	7	1305	1425	740567424	740567535	5.350000e-22	115.0
17	TraesCS4A01G490100	chr7D	95.356	926	40	1	1447	2369	2611249	2610324	0.000000e+00	1469.0
18	TraesCS4A01G490100	chr7D	91.991	924	71	1	1446	2369	3788305	3787385	0.000000e+00	1293.0
19	TraesCS4A01G490100	chr7D	92.057	919	70	1	1451	2369	2358996	2358081	0.000000e+00	1290.0
20	TraesCS4A01G490100	chr7D	81.538	975	104	47	428	1366	2612361	2611427	0.000000e+00	734.0
21	TraesCS4A01G490100	chr7D	85.783	415	47	6	207	612	3896699	3897110	1.680000e-116	429.0
22	TraesCS4A01G490100	chr7D	87.578	161	10	3	49	209	3896363	3896513	6.730000e-41	178.0
23	TraesCS4A01G490100	chr7D	95.588	68	2	1	1368	1435	2611400	2611334	8.950000e-20	108.0
24	TraesCS4A01G490100	chr7D	95.833	48	1	1	1	48	3896331	3896377	2.520000e-10	76.8
25	TraesCS4A01G490100	chr7A	89.958	478	48	0	880	1357	3285340	3285817	3.350000e-173	617.0
26	TraesCS4A01G490100	chr7A	88.668	503	50	3	863	1359	3634709	3634208	7.240000e-170	606.0
27	TraesCS4A01G490100	chr7A	81.134	811	91	35	235	1021	3215215	3214443	5.640000e-166	593.0
28	TraesCS4A01G490100	chr7A	90.385	208	11	3	1	208	3215651	3215453	5.020000e-67	265.0
29	TraesCS4A01G490100	chr7A	93.805	113	5	2	58	170	2003604	2003494	4.050000e-38	169.0
30	TraesCS4A01G490100	chr7A	100.000	41	0	0	207	247	3215267	3215227	2.520000e-10	76.8
31	TraesCS4A01G490100	chr7B	95.238	42	2	0	404	445	708487069	708487028	1.520000e-07	67.6

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS4A01G490100	chr4A	740455881	740458249	2368	True	4375.000000	4375	100.000000	1	2369	1	chr4A.!!$R1	2368
1	TraesCS4A01G490100	chr4A	741794978	741795905	927	True	1461.000000	1461	95.151000	1445	2369	1	chr4A.!!$R3	924
2	TraesCS4A01G490100	chr4A	741589050	741589977	927	False	1456.000000	1456	95.043000	1445	2369	1	chr4A.!!$F7	924
3	TraesCS4A01G490100	chr4A	739650677	739651603	926	False	1399.000000	1399	93.959000	1446	2369	1	chr4A.!!$F1	923
4	TraesCS4A01G490100	chr4A	741484653	741485579	926	True	1393.000000	1393	93.851000	1446	2369	1	chr4A.!!$R2	923
5	TraesCS4A01G490100	chr4A	742055956	742056882	926	False	1371.000000	1371	93.420000	1446	2369	1	chr4A.!!$F8	923
6	TraesCS4A01G490100	chr4A	740021192	740022713	1521	True	1048.500000	1430	93.274000	876	2355	2	chr4A.!!$R5	1479
7	TraesCS4A01G490100	chr4A	739860786	739861545	759	False	359.000000	603	87.131500	876	1425	2	chr4A.!!$F9	549
8	TraesCS4A01G490100	chr4A	739920382	739921829	1447	True	224.000000	292	80.731500	360	1109	2	chr4A.!!$R4	749
9	TraesCS4A01G490100	chr7D	3787385	3788305	920	True	1293.000000	1293	91.991000	1446	2369	1	chr7D.!!$R2	923
10	TraesCS4A01G490100	chr7D	2358081	2358996	915	True	1290.000000	1290	92.057000	1451	2369	1	chr7D.!!$R1	918
11	TraesCS4A01G490100	chr7D	2610324	2612361	2037	True	770.333333	1469	90.827333	428	2369	3	chr7D.!!$R3	1941
12	TraesCS4A01G490100	chr7D	3896331	3897110	779	False	227.933333	429	89.731333	1	612	3	chr7D.!!$F1	611
13	TraesCS4A01G490100	chr7A	3634208	3634709	501	True	606.000000	606	88.668000	863	1359	1	chr7A.!!$R2	496
14	TraesCS4A01G490100	chr7A	3214443	3215651	1208	True	311.600000	593	90.506333	1	1021	3	chr7A.!!$R3	1020

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
284	684	0.038599	TAGTACCGTGGCAGTCCTCA	59.961	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1937	3488	0.036875	GCTGGTACCACTTGAGCCTT	59.963	55.0	11.6	0.0	0.0	4.35	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	3.710722	CTCTGGCCCTGGAAGCGT	61.711	66.667	0.00	0.00	0.00	5.07
75	76	3.125316	GCGGTGACCTAGTCAGATTTTTG	59.875	47.826	0.00	0.00	43.57	2.44
82	83	9.654663	GTGACCTAGTCAGATTTTTGTATAGTT	57.345	33.333	0.00	0.00	43.57	2.24
166	167	1.662629	CTAGCCAAGACATCAAGCGTG	59.337	52.381	0.00	0.00	0.00	5.34
167	168	1.154150	GCCAAGACATCAAGCGTGC	60.154	57.895	0.00	0.00	0.00	5.34
168	169	1.855213	GCCAAGACATCAAGCGTGCA	61.855	55.000	0.00	0.00	0.00	4.57
169	170	0.110056	CCAAGACATCAAGCGTGCAC	60.110	55.000	6.82	6.82	0.00	4.57
170	171	0.587768	CAAGACATCAAGCGTGCACA	59.412	50.000	18.64	0.00	0.00	4.57
171	172	1.002576	CAAGACATCAAGCGTGCACAA	60.003	47.619	18.64	0.00	0.00	3.33
172	173	0.588252	AGACATCAAGCGTGCACAAC	59.412	50.000	18.64	8.30	0.00	3.32
173	174	0.588252	GACATCAAGCGTGCACAACT	59.412	50.000	18.64	10.75	0.00	3.16
284	684	0.038599	TAGTACCGTGGCAGTCCTCA	59.961	55.000	0.00	0.00	0.00	3.86
289	689	0.804989	CCGTGGCAGTCCTCATTTTC	59.195	55.000	0.00	0.00	0.00	2.29
380	784	2.441532	GCTCCATGTGCATGCCCT	60.442	61.111	16.68	0.00	37.49	5.19
451	856	7.279750	AGAGTCTCCTCGAAAGTAATAATCC	57.720	40.000	0.00	0.00	42.86	3.01
455	860	7.342284	AGTCTCCTCGAAAGTAATAATCCAAGA	59.658	37.037	0.00	0.00	0.00	3.02
458	863	7.046033	TCCTCGAAAGTAATAATCCAAGAACC	58.954	38.462	0.00	0.00	0.00	3.62
473	878	6.108015	TCCAAGAACCTACGCGTATTTTAAT	58.892	36.000	20.91	5.55	0.00	1.40
524	959	8.958506	GTACTACTACTCTTTCAAATCCAGAGA	58.041	37.037	2.46	0.00	37.97	3.10
550	1635	7.230027	AGATAAGAATCCAATGAGATTGTCCC	58.770	38.462	2.50	0.00	36.60	4.46
554	1639	3.198409	TCCAATGAGATTGTCCCATCG	57.802	47.619	0.00	0.00	38.59	3.84
577	1662	5.181245	CGGATTCCAGTGTTTGAAACTATGT	59.819	40.000	9.69	0.00	0.00	2.29
579	1664	7.065803	CGGATTCCAGTGTTTGAAACTATGTAT	59.934	37.037	9.69	4.30	0.00	2.29
614	1704	2.159296	GGCCAAGGTAATTAACAAGGCG	60.159	50.000	22.34	0.98	40.02	5.52
644	1735	2.748605	CCTAGCTAGGCAATCGACAAG	58.251	52.381	26.62	0.00	36.53	3.16

Showing 1 to 25 of 93 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	0.456221	AATCTGACTAGGTCACCGCG	59.544	55.000	0.00	0.00	37.67	6.46
167	168	0.751277	TTGGGAGGTGTGCAGTTGTG	60.751	55.000	0.00	0.00	0.00	3.33
168	169	0.185901	ATTGGGAGGTGTGCAGTTGT	59.814	50.000	0.00	0.00	0.00	3.32
169	170	1.331214	AATTGGGAGGTGTGCAGTTG	58.669	50.000	0.00	0.00	0.00	3.16
170	171	2.969821	TAATTGGGAGGTGTGCAGTT	57.030	45.000	0.00	0.00	0.00	3.16
171	172	3.456380	AATAATTGGGAGGTGTGCAGT	57.544	42.857	0.00	0.00	0.00	4.40
172	173	7.502226	TCTTATTAATAATTGGGAGGTGTGCAG	59.498	37.037	8.34	0.00	0.00	4.41
173	174	7.350382	TCTTATTAATAATTGGGAGGTGTGCA	58.650	34.615	8.34	0.00	0.00	4.57
284	684	4.157289	GTGACATGCACATGAGGAGAAAAT	59.843	41.667	17.19	0.00	46.91	1.82
289	689	3.810006	CACGTGACATGCACATGAGGAG	61.810	54.545	10.90	8.12	43.03	3.69
308	708	3.808466	TGCTCTCTATCACCACATCAC	57.192	47.619	0.00	0.00	0.00	3.06
320	720	3.956848	AGCACTCATGTGTATGCTCTCTA	59.043	43.478	6.97	0.00	45.11	2.43
402	806	2.260743	GAACGTCGACAGGGTCCC	59.739	66.667	17.16	0.00	0.00	4.46
451	856	8.663771	AAAATTAAAATACGCGTAGGTTCTTG	57.336	30.769	24.78	0.00	0.00	3.02
455	860	7.809665	ACTGAAAATTAAAATACGCGTAGGTT	58.190	30.769	24.78	20.83	0.00	3.50
524	959	7.723172	GGGACAATCTCATTGGATTCTTATCTT	59.277	37.037	1.50	0.00	44.42	2.40
550	1635	4.216257	AGTTTCAAACACTGGAATCCGATG	59.784	41.667	2.41	0.00	0.00	3.84
554	1639	6.575162	ACATAGTTTCAAACACTGGAATCC	57.425	37.500	2.41	0.00	0.00	3.01
577	1662	1.204146	GGCCTCTCCCACTCACAATA	58.796	55.000	0.00	0.00	0.00	1.90
579	1664	1.059584	TTGGCCTCTCCCACTCACAA	61.060	55.000	3.32	0.00	33.82	3.33
627	1717	1.134670	GTCCTTGTCGATTGCCTAGCT	60.135	52.381	0.00	0.00	0.00	3.32
628	1718	1.291132	GTCCTTGTCGATTGCCTAGC	58.709	55.000	0.00	0.00	0.00	3.42
629	1719	1.560923	CGTCCTTGTCGATTGCCTAG	58.439	55.000	0.00	0.00	0.00	3.02
630	1720	0.459585	GCGTCCTTGTCGATTGCCTA	60.460	55.000	0.00	0.00	0.00	3.93
644	1735	0.596577	TCCTCGTATGCTATGCGTCC	59.403	55.000	6.54	0.00	39.45	4.79

Showing 1 to 25 of 90 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.